There seems to be a common misunderstanding of what protest rights you have in the US. The first amendment does not give you the right to protest anything, at any point, in any manner that you want. In fact, the government has a duty to protect my rights if your protest in infringing on them. The Occupy movement is another group that completely failed to understand that fact. You are legally allowed to protest, but preventing someone from going to work or class is a quick way to get your protest shutdown. I don't think it is unreasonable to extend that same logic to DDoS attacks.
Civil disobedience is illegal by definition. DDoS attacks are illegal. Marching down the middle of the street is illegal. But are these acts immoral?
If they seriously infringe on the rights of other individuals, then yes I think they are immoral. Putting your own political motivations (no matter how righteous) above the rights of others is a selfish act.
Marching down the middle of the street is not illegal. Indeed, many fundamental cases of constitutional law note that the street is a "per se" public forum, i.e., the most public a forum can be, and is thus subject to the highest protections for speech.
Marching down a street and merely disrupting traffic is thus quite legal, however, if your marching causes dangerous disruptions to traffic (i.e., accidents), then it is not.
The easy answer if you want to march down the street is you tell city hall and get a parade permit. Did anybody tell MIT and apply for a packet storm permit?
Just don't expect sympathy from anyone you've inconvenienced when that right is infringed upon.
You can't assemble if it infringes on any one elses right to get to a public destination.